Some fields in defaultIndexConfiguration does not get indexed
We have Coveo 3.0 is intalled over Sitecore.NET 8.1 (rev. 160302)
I have two separate index field configurations under Coveo.SearchProvider.config and z_Custom/Coveo.SearchProvider.config. When I check showconfig.aspx I also see that defaultIndexConfiguration is indeed containing all fields not being overriden.
After doing a full reindex I see that _id and _templateid fields are not stored in index document. I also checked that these two fields are existing in RabbitMQ message.
Since your fields are in RabbitMQ messages and in your field set, but not on your documents, I think the easiest solution would be to open a support case with Coveo.